Search Results (252)

Background/Objectives: Vancomycin-resistant (VRE) and vancomycin-variable (VVE) Enterococcus spp. represent an increasing clinical challenge due to limited treatment options and the potential for undetected dissemination of such resistance genes. Data on Enterococci genomic epidemiology in healthcare settings remain rather limited. Our study aimed to investigate vancomycin resistance determinants in Enterococcus spp., clonal structure, and occurrence of VVE using whole-genome sequencing (WGS) in Latvia. Methods: Clinical isolates collected from hospitalised patients in two tertiary-level hospitals in Latvia (2021–2024) were analysed using WGS following routine laboratory identification. Vancomycin resistance determinants were identified in silico, along with MLST and cgMLST genotyping. Results: Of 532 sequenced isolates, 482 met the quality and inclusion criteria. E. faecalis (56.64%) and E. faecium (40.25%) predominated. Among 125 isolates carrying vancomycin resistance genes, vanB (54.40%) was the most frequent, followed by vanA (38.20%) and vanC (6.40%); vanC was restricted to E. gallinarum and E. casseliflavus. Vancomycin resistance was more prevalent in E. faecium (51.03%) than in E. faecalis (6.59%). cgMLST identified outbreak clusters among E. faecium ST80 and ST78 with complex type-specific resistance patterns and hospital specificity. E. faecalis showed polyclonal endemicity with the vanB gene present in different clades. Three (0.62%) vancomycin-variable E. faecium (VVE) isolates were identified in one hospital, harbouring vanA-type gene clusters comprising vanHAX but lacking the sensory gene vanS and the regulatory gene vanR. Conclusions: The VanB gene predominated in both hospitals, driven by clonal expansion of hospital-adapted E. faecium ST80/ST78, contrasting with earlier vanA predominance in Europe but aligning with recent regional vanB trends. The detection of VVE highlights clinically relevant genotype–phenotype discordance, underscoring the importance of integrating genomic surveillance with routine phenotypic testing to detect cryptic resistance and guide effective antimicrobial therapy. Full article

Microsporum canis is a globally prevalent zoonotic dermatophyte and the major causative agent of dermatophytosis in both pets and humans. The widespread clinical use of antifungal drugs has led to the frequent emergence of decreased susceptibility, while its molecular features and the genomic basis of cross-host transmission remain incompletely elucidated. In this study, 38 clinical M. canis isolates were collected from dogs and cats in Beijing (2025). We determined the minimum inhibitory concentrations (MICs) of six common antifungal agents via microbroth dilution, and performed whole-genome sequencing and comparative genomic analysis. All isolates showed high clonal homogeneity, with ANI $>99.9\%$ to the reference. A local human-derived strain was nested within the pet-derived clade, supporting zoonotic cross-host transmission. Terbinafine exhibited the highest activity, while itraconazole, voriconazole, posaconazole, griseofulvin, and ciclopirox olamine showed higher MICs; 11 isolates showed a multidrug high-MIC phenotype. Notably, copy number variation in the ABC transporter gene CDR1 was positively correlated with MICs of multiple antifungal agents ($p<0.05$). This study provides a genomic basis for optimized antifungal therapy, resistance surveillance and transmission control of zoonotic M. canis. Full article

Seasonal human influenza A viruses (H1N1 and H3N2) are frequently transmitted to swine populations. Continued transmission of these viruses among swine results in genetic and phenotypic changes, creating new lineages of swine influenza viruses that differ from their parent strains. This contributes to increased viral genetic diversity and the emergence of zoonotic risks. The aim of this study was to assess the prevalence of influenza viruses, including presumably human-origin A(H3N2) strains, on swine farms in Kazakhstan from 2022 to 2025. Real-time RT-PCR was used to test nasal swab antigens, and hemagglutinin inhibition test, and ELISA were used to determine serum antibody levels. Influenza A/H1N1 and A/H3N2 viruses, as well as the A(H7) hemagglutinin genes, were detected in swine. Serological analysis confirmed the presence of antibodies to the A/H1N1pdm09 and A/H3N2 viruses. The influenza A(H3N2) isolates were found to be genetically similar to human viruses of the J.2 or 3C.2a1b.2a.2a.3a.1 clade, possibly indicating transmission from humans to animals. The ongoing exchange of influenza viruses between humans and swine poses a threat of future pandemics. These studies highlight the need for continuous monitoring of swine influenza in Kazakhstan to understand virus evolution and protect public health. Full article

Lumpy Skin Disease (LSD) is an economically significant viral disease of cattle, widely prevalent across Africa, particularly in sub-Saharan regions. In 2024, Tunisia reported its first outbreak. Understanding the genetic characteristics of lumpy skin disease virus (LSDV) and related poxviruses is critical for surveillance and control. Twenty-nine samples from 26 suspected cases were screened for LSDV using qPCR, followed by a High-Resolution Multiplex Melting (HRM) assay. Three representative samples, two LSDV-positive and one bovine papular stomatitis virus (BPSV)-positive, were subjected to whole-genome sequencing using Pacific Biosciences (PacBio) HiFi long-read technology. Phylogenetic analyses of the LSDV-marker gene RPO30 and complete genomes were performed alongside SNP and InDel profiling. The Tunisian LSDV isolates clustered with Clade 1.2.2 field strains and were 100% identical to each other and to the Italian isolate LSDV_Italy_Sardinia_2025, sharing 99.99% nucleotide identity with LSDV_V281_Nigeria. Although only two LSDV isolates were sequenced which showed no genetic differences, these findings suggest genomic stability within Clade 1.2.2. The Tunisian BPSV isolate showed high similarity (98.15–98.59%) to strains reported in Germany and Switzerland. This study presents the first genetic characterization of LSDV and BPSV in Tunisia, highlighting the importance of accurate differential diagnosis among poxviruses and continuous genomic surveillance to inform control strategies. Full article

Objective: The aim of this study was to characterize the epidemiological features and whole-genome characteristics of H5 subtype avian influenza viruses circulating in Jining City during 2024–2025, and to provide scientific evidence for avian influenza prevention and control. Methods: A total of 748 poultry-related environmental samples were collected in March, June, September, and December of 2024–2025. Reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) was used to detect influenza A virus and H5 subtype viral RNA. H5-positive samples were subjected to whole-genome sequencing and analyzed using bioinformatics tools. Results: Among the 748 samples, the positivity rate of influenza A virus was 16.04% (120/748), and that of the H5 subtype was 8.16% (61/748). The H5 positivity rate in 2025 (11.88%) was significantly higher than that in 2024 (5.37%). Higher positivity rates were observed in March and December compared to June and September. Twelve complete H5 genomes were obtained, including nine H5N1 and three H5N6 strains. All HA genes belonged to clade 2.3.4.4b. Key mutations related to antigenic drift, replication and adaptation were detected in multiple viral proteins. Conclusions: The positivity rate of H5 subtype avian influenza viruses in Jining City showed an increasing trend during 2024–2025, with higher prevalence in winter and spring. The circulating strains predominantly belonged to clade 2.3.4.4b. Antigenic drift-associated mutations in the HA protein were identified in some strains, which may affect vaccine matching. Enhanced surveillance of H5 viruses and regular evaluation of antigenic compatibility between vaccine and circulating strains are recommended to mitigate potential risks posed by viral genetic variation. Full article

C. difficile is a major cause of antibiotic-associated diarrhea and hospital-acquired infections, although increasing community-acquired cases suggest alternative transmission routes. Livestock, particularly pigs, have been proposed as potential reservoirs. This study aimed to investigate the presence of zoonotic ribotypes in piglets from Tenerife (Spain) and to assess their pathogenic potential by detecting toxin genes. A total of 140 samples were analyzed, including 58 fecal samples from slaughtered piglets (4–8 weeks old) and 82 rectal swabs from piglets aged 2–25 days. Samples were cultured, identified by MALDI-TOF MS, and characterized by PCR ribotyping and toxin gene detection. No isolates were obtained from fecal samples collected at slaughter, whereas 14 (17%) rectal swabs were positive. Colonization was strongly age-dependent, with the highest prevalence at 2 days of age (100%), decreasing by day 9 (10.7%), and absent after 21 days (p < 0.05). All isolates were ribotype RT033 with a tcdA⁺/tcdB⁻/cdtA⁺/cdtB⁺ profile. The exclusive detection of RT033, a clade V lineage linked to animal reservoirs and occasional human infections, suggests a potential zoonotic risk, especially for farm workers. These findings reinforce the need for integrated C. difficile surveillance under a One Health framework to monitor emerging ribotypes and their role in community-acquired infections. Full article

Vanilla planifolia, a high-value tropical orchid, is significantly impacted by viral pathogens that threaten its cultivation and productivity. This study employs metagenomic techniques to detect and characterize the viral communities associated with V. planifolia in South Florida. Using high-throughput RNA sequencing, the Cymbidium mosaic virus (CymMV) and Vanilla latent virus (VLV) were prevalent in the plant system, with CymMV being the dominant viral species. Phylogenetic analysis of the CymMV coat protein gene revealed notable genetic divergence in the Homestead isolate, forming a distinct clade from global reference strains, suggesting local adaptation or host-specific evolution. Viral distribution across the plant system revealed higher viral loads in stem tissue, consistent with their role in systemic transport, whereas leaves exhibited greater viral richness, likely due to increased environmental exposure. The low abundance of other viral species, including Garlic viruses and Senna severe yellow mosaic virus, suggests that V. planifolia may harbor a broader range of viral taxa than previously characterized, though these findings represent a preliminary survey of symptomatic plants rather than a comprehensive regional assessment. This study underscores the value of metagenomic approaches for uncovering both well-characterized and novel viruses in plant systems and highlights the need for expanded sampling and continuous viral surveillance to guide disease management strategies in economically important crops such as vanilla. Full article

Background/Objectives: The emergence of antimicrobial-resistant (AMR) pathogens in aquaculture ecosystems poses a significant risk to both food security and human health. Shewanella species are recognized as significant AMR reservoirs, yet their prevalence and resistance mechanisms within a shrimp-related ecosystem remain poorly characterized. This study aimed to perform a genotypic and phenotypic characterization of S. algae VK101, isolated from wild-caught black tiger shrimp (Penaeus monodon) broodstock. Methods: A complete 5.21 Mb genome was generated using a hybrid Illumina and Oxford Nanopore sequencing approach. Antimicrobial susceptibility was evaluated for 21 antibiotics via Minimum Inhibitory Concentration (MIC) testing. Comparative pangenomics and genome-wide association studies (GWAS) across 125 S. algae genomes were conducted to identify novel resistance determinants. Results: MIC analysis revealed that VK101 was resistant to ampicillin (>16 µg/mL) and colistin (8 µg/mL), while showing intermediate susceptibility to imipenem and ciprofloxacin. In silico analysis identified 205 antimicrobial resistance genes (ARGs), including a perfect hit for the fluoroquinolone resistance gene qnrA3. Notably, no mcr genes were detected. Although VK101 exhibited moderate resistance (8 µg/mL), GWAS across the broader S. algae population linked a specific lptA mutation (K140N) to high-level resistance (64 µg/mL). Other GWAS-identified genes (e.g., czcA, ampC, and oprM) likely represent indirect associations driven by genetic linkage or clade-specific markers rather than direct causal factors. Conclusions: These findings highlighted the presence of multidrug-resistant S. algae in wild-caught P. monodon broodstock, reflecting the occurrence of antimicrobial resistance in aquatic environments. Colistin resistance in these isolates was primarily mediated by chromosomal variants rather than mobile mcr elements, indicating the need for integrated genomic surveillance within the aquaculture value chain. Full article

Influenza viruses are significant causes of acute respiratory infections, often leading to severe health issues and mortality. These viruses undergo continuous mutations and genetic reassortments, resulting in annual epidemics and potential pandemics. The A(H3N2) strains exhibit high genetic and antigenic variability, that influence vaccine efficacy. This study aimed to assess the prevalence of influenza viruses, including A(H3N2) strains, in Kazakhstan during 2020–2025. The study used nasopharyngeal swab and serum samples obtained from patients. The presence of influenza virus antigens in nasopharyngeal swabs was analyzed using real-time polymerase chain reaction. The level of specific antibodies in the blood serum was determined using the hemagglutination inhibition reaction and enzyme-linked immunosorbent assay methods. Influenza A/H1N1, A/H3N2 and B viruses were diagnosed using real-time PCR. Antibodies to A/H1N1pdm09, A/H3N2 and B were detected in serological studies. Our studies revealed a trend toward seasonal patterns in influenza A viruses circulation. Therefore, it was established that the A/H3N2 strains dominated in Kazakhstan during the 2021–2022 and 2023–2024 epidemic seasons. The 2023–2024 strains belong to the specific genetic clade J.2 or 3C.2a1b.2a.2a.3a.1. These studies confirmed the role of influenza viruses in the etiology of respiratory infections and emphasized the need to continue monitoring their spread in Kazakhstan. Full article

Background/Objectives: Influenza, RSV, and SARS-CoV-2 co-circulate and evolve under immune and therapeutic pressures, complicating decision-making for both vaccine formulation and antiviral use. Fragmented, pathogen-specific sequencing approaches limit cross-virus comparability. Methods: We applied a standardized, multiplexed, amplicon-based next-generation sequencing (NGS) workflow to 34 diagnostic specimens (Ct < 35) positive for influenza A/B, RSV-A/B, or SARS-CoV-2. Sequencing libraries were generated and run on an Illumina MiSeq platform (2 × 250 bp). Although the wet-lab workflow is standardized across pathogens, consensus generation and annotation utilized two different analysis environments: Geneious Prime for influenza and MicrobioChek for RSV and SARS-CoV-2. Quality metrics included genome breadth and depth of coverage. Results: Near-complete genomes (mean coverage ≥98%) were recovered for all samples. Influenza A(H1N1)pdm09 sequences clustered in clade 6B.1A; A(H3N2) clustered in subclade 3C.2a1b.2a.2; and influenza B belonged to the Victoria lineage V1A.3a.2. RSV sequences were assigned to Nextclade clades A.D.5.1, A.D.1.10, A.D.2.1, and A.D.3 (RSV-A) and to B.D.4.1.3 and B.D.E.1 (RSV-B), consistent with the ON1 (RSV-A) and BA (RSV-B) genotypes prevalent in recent seasons. Clinically relevant mutations included changes in the influenza HA site and neuraminidase substitutions, RSV F-protein polymorphisms, and spike protein substitutions associated with recent Omicron sublineages (L455F/S, F456L) in SARS-CoV-2. Conclusions: A unified amplicon–NGS approach yields harmonized genomic data across respiratory viruses, enabling timely detection of antigenic drift and resistance markers while supporting integrated, cross-pathogen surveillance. Full article

PRRSV-2 represents a major threat to the swine industry. Canada is one of the world’s leading pork producers and a major trading partner of live pigs with the United States, yet PRRSV-2 evolutionary dynamics in these two countries are often studied independently, partly due to limited publicly available sequence data from Canada. We analyzed more than 3000 PRRSV-2 ORF5 sequences collected between 2000 and 2024 from five Canadian provinces. Thirteen previously described sub-lineages were detected in Canada, while approximately one-third of the sequences could not be assigned to any known sub-lineage. Phylogenetic analyses incorporating global reference sequences revealed that most unclassified sequences clustered into four distinct monophyletic clades, exhibiting genetic distances greater than 9.5% from recognized sub-lineages. We propose two new sub-lineages, 1K and 1L, corresponding to clades that were prevalent and persistent over time, whereas the remaining two clades were rare and last detected in 2021. We reconstructed cross-border transmission histories and found that sub-lineages 1C, 1H, 1I, 1K, and 1L originated in Canada, whereas 1A, 1B, 1E, and 1F originated in the United States. Transmission patterns varied across sub-lineages, ranging from unidirectional to bidirectional movement. Our findings refine PRRSV-2 classification and provide insights to inform targeted surveillance, particularly at national borders. Full article

Passion fruit (Passiflora edulis Sims) is an important economic fruit crop in Rwanda grown for both domestic consumption and export markets. However, viral diseases pose a significant threat to passion fruit production. Among these, passion fruit woodiness disease (PWD) is the most destructive, causing yield losses of up to 100%. A survey was carried out to assess the distribution of Ugandan passiflora virus (UPV; Potyvirus passiflorafricanse) in major passion fruit growing areas. UPV is one of the major viruses known to cause PWD. The incidence of viral symptoms observed in the field did not differ significantly among districts, ranging from 81% in Rusizi to 100% in Rwamagana. However, mean symptom severity scores varied significantly between districts, with the highest severity recorded in Kayonza (3.1) and the lowest in Rulindo (1.9). Serological analysis detected potyviruses in 44% of the total samples (n = 216), including 43% of symptomatic (n = 144) and 47% of asymptomatic (n = 72) leaf samples collected from passion fruit fields. Further analysis using Reverse-Transcription Polymerase Chain Reaction (RT-PCR) detected UPV in 56% of symptomatic (n = 126) and 53% of asymptomatic (n = 60) samples, corresponding to 55% of the total samples tested (n = 186). The virus was present in all surveyed districts, with UPV infection prevalence of 89% in Rusizi, 75% in Rwamagana, 74% in Karongi, 59% in Nyamagabe, 44% in Nyaruguru, 38% in Kayonza, and 30% in both Gakenke and Rulindo. Fifteen partial coat-protein gene sequences for the Rwandan isolates were obtained. The newly described Rwandan isolates shared 97–99% nucleotide (nt) identity with one another, 89–94% with previously reported Rwandan isolates, 81–97% with Ugandan isolates, and 80–82% with Kenyan UPV isolates, suggesting that the Rwandan virus population is relatively homogenous. Genetic distances among the 15 new UPV isolates and previously reported Rwandan, Ugandan, and Kenyan isolates were very short (0.01–0.03), indicating high sequence similarity. All Rwandan isolates clustered into a single major clade, together with some Ugandan and Kenyan isolates. This close genetic relationship suggests a common ancestry and the regional spread of a single dominant UPV lineage. These findings highlight the need to reinforce seed and planting-material certification systems, as well as the need to enhance farmer capacity through targeted training on viral disease identification and management practices. This is vital to limiting the spread of viral diseases that threaten income security among smallholder passion fruit farmers. Full article

Enterocytozoon bieneusi is a microsporidian species found ubiquitously in both invertebrate and vertebrate hosts including domestic and wild animals and humans. Enterocytozoon bieneusi typically causes severe or chronic diarrhea, malabsorption and emaciation. This study aimed to investigate the prevalence and genotypic distribution of E. bieneusi in dogs in Fujian province, China. A total of 506 fecal samples from dogs were randomly collected from eight districts in Fujian province, China. The presence of E. bieneusi was confirmed through nested PCR targeting ITS gene. Further multilocus sequence typing (MLST) focused on the three microsatellite loci (MS1, MS3, and MS7) and minisatellite locus (MS4) loci. As a result, the infection rates of E. bieneusi in dogs were found to be 5.93% (30/506). A highly significant difference in the prevalence of E. bieneusi was observed across different urban areas (p < 0.01), with Longyan city exhibiting the highest infection rate (24.62%, 16/65), Zhangzhou and Xiamen the lowest (0.00%). Prevalence also varied significantly by source (p < 0.01), age (p < 0.01), gender (p < 0.05), symptom status (p < 0.01), and season (p < 0.01). Three known genotypes of E. bieneusi were identified in 30 dogs’ positive samples, including EbpC, PigEBITS5 and PtEb IX, whereas FJLYD1, FJLYD2 and FJSMD have been identified as new genotypes. EbpC, PigEBITS5, FJLYD1, FJLYD2, and FJSMD all belong to Group 1, while PtEb IX is assigned to Group 11. Genotypes belonging to Group 1, the first major phylogenetic clade, are considered to possess potential zoonotic risks. None of the positive samples amplified at all four loci, forming a single multilocus genotype (MLG). This study contributes to a deeper understanding of E. bieneusi in dogs, which provides critical data for the development of targeted control strategies in Fujian province. Full article

The aim of the study was to investigate the MLST types and genes encoding Clostridioides difficile toxins from fecal clinical samples of patients from two large Bulgarian cities. Overall, 100 toxigenic isolates were obtained during a 10-year period from five hospitals in Sofia and Varna, Bulgaria. Toxin gene patterns of the isolates were determined with conventional polymerase chain reaction, and multilocus sequence typing (MLST) types were determined according to Griffith’s scheme. The evolutionary relatedness of ST types was analyzed through PHYLOViZ. Binary toxin-positive isolates accounted for 35% (35/100), and the most prevalent sequence type (ST) type was ST1 (clade2) with 34%. One binary toxin-positive isolate belonged to ST11 (clade5). The cdt-negative isolates were of two clades: clade 4 (ST37), with 1 tcdA-tcdB+ isolate, and clade 1, with 64 isolates. All the cdt-positive isolates showed 18 bp deletions of tcdC, except a ST11 isolate exhibiting a 39 bp deletion. Importantly, there was more than a 6-fold increase in ST1 isolates in the 2020–2023 period versus 2014–2019. The main cdt-negative isolates were ST3 (14%), ST2 (6%), ST42 (5%), and ST92 (5%). They were tcdA+tcdB+. Four main clonal complexes (with one allele difference) were found. The first one encompassed 19 isolates and included ST3 and ST42; the second included ST8, ST16, ST52, ST92 and ST36 (11 isolates); the third consisted of 13 isolates (ST2, ST49, ST13 and ST110 clones); and the fourth included ST10 and ST44 (5 isolates). The significance of our work is the detection of a high frequency of hypervirulent isolates during the COVID-19 pandemic period, which we attribute to the national consumption of systemic antibiotics, which increased during the second period, unlike the trend in other European countries. The results highlight the need for enhanced infection control measures and strict compliance with antibiotic stewardship programs. Full article

The avian immunosuppressive and neoplastic diseases are great threats to the poultry industry, causing huge economic losses worldwide. Most recently, the emerging hypervirulent variants of Marek’s disease virus (HV-MDV), partially co-infected with avian leukosis virus (ALV) and/or reticuloendotheliosis virus (REV), have been identified as the key driver of tumour outbreaks in vaccinated chicken flocks, but the role of chicken infectious anemia virus (CIAV) remains unclear. Herein, we have investigated the prevalence and co-infection of CIAV in 71 clinical tumour-bearing flocks collected from central China during 2021–2023, which has shown a CIAV positivity rate of 59.2% (42/71). Notably, the incidence of CIAV mono-infection increased significantly from 0% (0/29) in 2021 to 23.7% (9/38) in 2023, whereas CIAV + MDV co-infection decreased from 65.5% (19/29) to 31.6% (12/38). A total of 20 viral genomes of epidemic CIAV isolates from diverse sources were obtained, and the phylogenetic analysis, including 91 reference isolates were clustered into four major lineages (A–D), with clade C further subdivided into subclades C1 and C2. Clade C1 consisted predominantly of Asian isolates, with 88.5% (46/52) of the isolates originating from mainland China. Among the 20 new isolates, 17 were clustered in subclade C1, two in C2, and one in B. The VP1 gene phylogeny showed a topology largely consistent with that of the whole-genome analysis. Moreover, all newly characterized isolates contained glutamine (Q) at VP1 residue 394, a molecular marker associated with high pathogenicity. Collectively, our data suggest that prevalent HV-MDV variants together with CIAV co-infections are the primary drivers of the ongoing tumour outbreaks in Chinese poultry flocks. Notably, the significantly increased CIAV mono-infections, possibly resulting from an independently evolving lineage among circulating Chinese strains, are likely to pose a new challenge for future control of disease. Full article